LAMMPS (18 Feb 2013)
# 2d indenter simulation

dimension	2
boundary	p s p

atom_style	atomic
neighbor	0.3 bin
neigh_modify	delay 5

# create geometry

lattice		hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region		box block 0 20 0 10 -0.25 0.25
create_box	2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
  1 by 1 by 1 MPI processor grid
create_atoms	1 box
Created 420 atoms

mass		1 1.0
mass		2 1.0

# LJ potentials

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0 2.5

# define groups

region	        1 block INF INF INF 1.25 INF INF
group		lower region 1
60 atoms in group lower
group		mobile subtract all lower
360 atoms in group mobile
set		group lower type 2
  60 settings made for type

# initial velocities

compute	  	new mobile temp
velocity	mobile create 0.2 482748 temp new
fix		1 all nve
fix		2 lower setforce 0.0 0.0 0.0
fix		3 all temp/rescale 100 0.1 0.1 0.01 1.0

# run with indenter

timestep	0.003
variable	k equal 1000.0/xlat
variable        y equal "13.0*ylat - step*dt*0.02*ylat"

fix		4 all indent $k sphere 10 v_y 0 5.0
fix		4 all indent 882.84928691481343321 sphere 10 v_y 0 5.0
fix		5 all enforce2d

thermo		1000
thermo_modify	temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)

#dump		1 all atom 250 dump.indent

#dump		1 all image 1000 image.*.jpg type type #		zoom 1.6 adiam 1.5
#dump_modify	1 pad 5

run		30000
Memory usage per processor = 2.05951 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0          0.2   -3.1727576            0   -3.0018052    -1.436185    444.53333 
    1000   0.11974254   -3.0876892            0   -2.9853378 -0.037059247    440.78771 
    2000   0.12086797   -3.0886512            0   -2.9853378  -0.39883289     444.3556 
    3000   0.11671309   -3.0840074            0   -2.9842455  -0.34859991    442.95428 
    4000   0.12339115   -3.1000529            0   -2.9945828 -0.049696765    438.99297 
    5000   0.10860594   -3.0866045            0   -2.9937722  -0.47973882    443.99855 
    6000   0.11839788   -3.0929689            0   -2.9917669 -0.033454196    442.70339 
    7000   0.12194527   -3.0835584            0   -2.9793242  -0.13981611    443.36261 
    8000   0.11671309   -3.0862884            0   -2.9865265  0.073952568    441.71327 
    9000   0.12449823   -3.0880806            0   -2.9816643   0.28647997    439.28167 
   10000   0.12475263   -3.0830722            0   -2.9764384   0.38101457    440.50309 
   11000   0.11198118   -3.0743549            0   -2.9786377   0.67583952    438.50252 
   12000   0.10823034   -3.0621355            0   -2.9696244   0.66485024    441.13781 
   13000    0.1194298   -3.0579575            0   -2.9558734    1.0884087    437.72805 
   14000   0.12310403    -3.051382            0   -2.9461573   0.87077702    445.54011 
   15000   0.11148462   -3.0402208            0    -2.944928    1.0040645    451.90788 
   16000   0.12322336    -3.041552            0   -2.9362254   0.75818852    456.90372 
   17000   0.12311109    -3.030034            0   -2.9248033    1.0483105    452.91666 
   18000   0.12062529   -3.0261654            0   -2.9230595    1.3983601    451.71885 
   19000   0.11959344   -3.0143076            0   -2.9120837    1.3960449     457.9261 
   20000   0.12233862   -3.0015922            0   -2.8970218    1.1237129      470.124 
   21000   0.12097317   -3.0284929            0   -2.9250896   0.76635797    472.92527 
   22000   0.11569678   -3.0270581            0   -2.9281649    0.5809488    474.70546 
   23000    0.1108732   -3.0266318            0   -2.9318616   0.98885909    471.32905 
   24000   0.12620366   -3.0324956            0   -2.9246215    1.0953962    467.09873 
   25000   0.12180898   -3.0158998            0   -2.9117821    1.0327326    468.77165 
   26000   0.11188975   -3.0111933            0   -2.9155542    1.0566079    475.00383 
   27000   0.11592811   -3.0033529            0   -2.9042619    1.0702439    475.46225 
   28000   0.12257955   -2.9963958            0   -2.8916195    1.3711735    474.37327 
   29000   0.11235575   -2.9779653            0   -2.8819279    1.5993236    472.45721 
   30000   0.11564816   -2.9764576            0    -2.877606    1.7153154     475.9608 
Loop time of 2.3314 on 1 procs for 30000 steps with 420 atoms

Pair  time (%) = 1.73976 (74.6228)
Neigh time (%) = 0.0687068 (2.94702)
Comm  time (%) = 0.0318851 (1.36764)
Outpt time (%) = 0.000296593 (0.0127217)
Other time (%) = 0.490756 (21.0498)

Nlocal:    420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    110 ave 110 max 110 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3729 ave 3729 max 3729 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3729
Ave neighs/atom = 8.87857
Neighbor list builds = 619
Dangerous builds = 0

# run without indenter

unfix           4
run		30000
Memory usage per processor = 2.05959 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
   30000   0.11564816   -2.9764576            0    -2.877606    1.7186102    475.04831 
   31000   0.11109883   -3.0337933            0   -2.9388303  -0.62530288     488.2277 
   32000    0.1188179   -3.0275826            0   -2.9260216  -0.66828105    485.94533 
   33000   0.11802002   -3.0512943            0   -2.9504153   0.25566016    476.02668 
   34000   0.10576299   -3.0406973            0   -2.9502951  -0.52852395    476.92361 
   35000   0.11793262   -3.0680565            0   -2.9672522   -0.4355881    468.95111 
   36000   0.12287931   -3.0867004            0   -2.9816678  0.062228809    461.41252 
   37000   0.11137578   -3.0739118            0    -2.978712  -0.71966265    470.33395 
   38000   0.11463317   -3.0653157            0   -2.9673316  -0.26573651    468.14603 
   39000   0.11376942   -3.0832959            0   -2.9860501 -0.015297443    460.99165 
   40000   0.11547074   -3.0745917            0   -2.9758917  -0.65392557    471.44699 
   41000   0.12353792   -3.0814892            0   -2.9758937   -0.2846897    464.57095 
   42000   0.11025924   -3.0833464            0    -2.989101 -0.092947795    462.24163 
   43000   0.11612511   -3.0669276            0   -2.9676682  -0.57569445    468.19807 
   44000   0.12120248   -3.0818096            0   -2.9782103  0.005877698    462.28926 
   45000   0.11846418   -3.0794698            0   -2.9782112  -0.27859792    465.42685 
   46000   0.11315369   -3.0749275            0    -2.978208  -0.65492669    469.71888 
   47000   0.11170116    -3.073688            0   -2.9782101  0.069117813     463.8082 
   48000   0.11853841   -3.0795346            0   -2.9782125  -0.64585424    467.42305 
   49000   0.10976733   -3.0727734            0   -2.9789485  -0.34654008    466.39102 
   50000   0.11671309   -3.0787137            0   -2.9789518  -0.10105418     462.8133 
   51000   0.10907083   -3.0715934            0   -2.9783638   -0.5708327    467.88839 
   52000   0.12514884   -3.0753206            0   -2.9683482  -0.20691236    464.84118 
   53000   0.12024322   -3.0851757            0   -2.9823964  -0.17603398     462.1454 
   54000    0.1194586   -3.0713797            0   -2.9692711  -0.44966799    466.03415 
   55000   0.12751859   -3.0782662            0   -2.9692682  -0.30626509    464.20394 
   56000   0.11163288   -3.0776391            0   -2.9822196  -0.27414403    466.07964 
   57000   0.12313114   -3.0705777            0   -2.9653298  -0.51276983    469.08858 
   58000   0.12589682    -3.084674            0   -2.9770622  -0.28711084    464.73702 
   59000   0.10936357   -3.0705365            0   -2.9770567  -0.33561843    464.63316 
   60000   0.12149574   -3.0809095            0   -2.9770596   -0.3776745     465.8276 
Loop time of 2.10947 on 1 procs for 30000 steps with 420 atoms

Pair  time (%) = 1.71534 (81.3161)
Neigh time (%) = 0.0708265 (3.35755)
Comm  time (%) = 0.0313859 (1.48786)
Outpt time (%) = 0.00027895 (0.0132237)
Other time (%) = 0.291641 (13.8253)

Nlocal:    420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3569 ave 3569 max 3569 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3569
Ave neighs/atom = 8.49762
Neighbor list builds = 641
Dangerous builds = 0
